SCPortalen

SCPortalen

A resource for the single-cell research community-

Single-cell omics recently emerged as powerful tools to investigate heterogeneity of large populations of cells. Among others, improvements in sequencing, microscopy and microfluidic technologies let to a rapid increase of complex datasets with single-cell resolution. However, due to a lack of available platforms to easily share and integrate complex single-cell datasets, the accessibility of such datasets can be a barrier to efficient usage.
To address the issue of efficient single-cell data management, we introduced a single-cell data integration platform. The motivation for the development of this database was to enable easy access, integration and collaboration on single-cell datasets generated by the research community worldwide. This database features integration of single-cell metadata, cell images and sequence information. Currently the platform is divided into two parts; the first part is the single-cell dataset generated at the Division of Genomic Technologies at RIKEN CLST and the second part is the single-cell dataset published in peer-reviewed journals.



Use theQuick Search Tableto browse our curated datasets.
Dataset Accession Number Dataset Title Organism Dataset Source Dataset Owner Cell Count
balbc_pbmc_5gex PBMCs from BALB/c mice - 5’ gene expression Mus musculus 10X Genomics 10X Genomics 8000
B_postvax_5gex_B Human B cells from a healthy donor post-flu vaccination (v2) Homo sapiens 10X Genomics 10X Genomics 8807
DRA001287 Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment. Homo sapiens Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo The University of Tokyo 337
DRA002399 Single-cell RNA-seq analysis of the cell cycle. Homo sapiens RIKEN Division of Genomic Technologies. RIKEN_CLST_DGT 472
DRA002730 Single cell analysis of lung adenocarcinoma cell lines and the response to an anti-cancer drug stimulation. Homo sapiens Laboratory of Functional Genomics The University of Tokyo UT-MGS 255
E-MTAB-2512 Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis Mus musculus Wellcome Trust Genome Campus EMBL-EBI 96
E-MTAB-2600 Single cell mRNA -sequencing reveals cell-to-cell variation in three mouse ES cell culture conditions Mus musculus Wellcome Trust Genome Campus EMBL-EBI 869
E-MTAB-2805 Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells Mus musculus Helmholtz Zentrum München–German Research Center for Environmental Health, Institute of Computational Biology EMBL-EBI 288
E-MTAB-3346 Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Mus musculus EMBL Heidelberg EMBL Heidelberg 341
E-MTAB-3543 Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Mus musculus EMBL-EBI EMBL-EBI 20
E-MTAB-3857 T cell fate and clonality inference from single-cell transcriptomes. Mus musculus EMBL-EBI EMBL-EBI 272
E-MTAB-3929 Single-cell RNA-seq reveal lineage formation and X-chromosome dosage compensation in human preimplantation embryos. Homo sapiens Karolinska Institutet Karolinska Institutet 1529
E-MTAB-4026 Single-cell RNA sequencing of mouse embryos with Tal1 (Scl) knockout. Mus musculus The University of Cambridge EMBL-EBI 768
E-MTAB-4079 Mouse embryonic RNA-seq. Mus musculus The University of Cambridge EMBL-EBI 1205
E-MTAB-4619 Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Mus musculus EMBL-EBI EMBL-EBI 287
E-MTAB-5060 Whole-islet RNA-sequencing analysis of human pancreas from healthy individuals and type 2 diabetes patients. Homo sapiens Karolinska Institutet Karolinska Institutet 7
E-MTAB-5061 Single-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patients. Homo sapiens Karolinska Institutet Karolinska Institutet 3514
fixed_neurons 2k Fixed Brain Cells from an E18 Mouse Mus musculus 10X Genomics 10X Genomics 2300
fixed_neurons_6days 2k Fixed (for 6 days at -80ºC) Brain Cells from an E18 Mouse Mus musculus 10X Genomics 10X Genomics 2520
GSE143607 Single-cell transcriptome analysis revealed continuous changes in molecular phenotypes during epithelial-to-mesenchymal transition Homo sapiens RIKEN IMS RIKEN IMS 8832
GSE29087 Characterization of the single-cell (ES and MEF) transcriptional landscape by highly multiplex RNA-Seq. Mus musculus Karolinska Institutet Karolinska Institutet 480
GSE36552 Initiation of a conserved trophectoderm program in human, cow and mouse embryos. Homo sapiens Peking University Peking University 124
GSE38495 Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Mus musculus and Homo sapiens Karolinska Institutet Karolinska Institutet 121
GSE41265 Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Mus musculus New York Genome Center New York Genome Center 68
GSE42268 Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Mus musculus RIKEN RIKEN 77
GSE45719 Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Mus musculus Karolinska Institutet Karolinska Institutet 317
GSE46980 Quantitative single-cell RNA-seq with unique molecular identifiers. Mus musculus Karolinska Institutet Karolinska Institutet 288
GSE48968 Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Mus musculus New York Genome Center New York Genome Center 4894
GSE51254 Quantitative assessment of single-cell RNA-sequencing methods. Homo sapiens Stanford University Stanford University 109
GSE52529 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Homo sapiens Harvard University Harvard University 372
GSE53386 Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Mus musculus and Homo sapiens Peking University Peking University 116
GSE54695 Validation of noise models for single-cell transcriptomics. Mus musculus Max Planck Institute of Immunobiology and Epigenetics Max Planck Institute of Immunobiology and Epigenetics 16
GSE56638 Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. Mus musculus The University of Pennsylvania The University of Pennsylvania 121
GSE57872 Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Homo sapiens Massachusetts General Hospital Massachusetts General Hospital 875
GSE59114 Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Mus musculus Broad Institute Broad Institute 2128
GSE59739 Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Mus musculus Karolinska Institutet Karolinska Institutet 2400
GSE60361 A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Mus musculus Karolinska Institutet Karolinska Institutet 3492
GSE63576 Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity. Mus musculus Shanghai Institute for Biological Sciences Chinese Academy of Sciences 209
GSE64016 Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Homo sapiens Morgridge Institute for Research Morgridge Institute for Research 460
GSE65360 Single-cell chromatin accessibility reveals principles of regulatory variation. Mus musculus and Homo sapiens Broad Institute Broad Institute 1920
GSE67310 Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Mus musculus Stanford University Stanford University 405
GSE68981 Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Mus musculus Yale University Yale University 519
GSE69405 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Homo sapiens Samsung Medical Center Samsung Genome Institute 201
GSE70151 Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Homo sapiens Harvard Medical School Harvard Medical School 192
GSE70245 Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Mus musculus Cincinnati Childrens Hospital Medical Center Cincinnati Childrens Hospital Medical Center 675
GSE70580 The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Homo sapiens Uppsala University Uppsala University 648
GSE70657 Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells. Mus musculus Weatheral Institute of Molecular Medicine Weatheral Institute of Molecular Medicine 135
GSE70798 Aire controls gene expression in the thymic epithelium with ordered stochasticity. Mus musculus Harvard Medical School Harvard Medical School 310
GSE71453 Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons. Mus musculus University of California Los Angeles University of California, Los Angeles 123
GSE71485 Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. Mus musculus Johns Hopkins University Johns Hopkins University 173
GSE71585 Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Mus musculus Allen Institute for Brain Science Allen Institute for Brain Science 1809
GSE73121 Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma. Homo sapiens Samsung Medical Center Samsung Genome Institute 121
GSE73727 Artemisinins Target GABA A Receptor Signaling and Impair alpha Cell Identity. Homo sapiens CeMM Research Center for Molecular Medicine Austrian Academy of Sciences 72
GSE74155 Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation. Mus musculus Karolinska Institutet Karolinska Institutet 617
GSE74672 Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Mus musculus Karolinska Institutet Karolinska Institutet 3077
GSE74833 Simulating multiple faceted variability in single cell RNA sequencing. Mus musculus EECS-UC Berkeley UC Berkeley 768
GSE75330 Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Mus musculus Karolinska Institutet Karolinska Institutet 6283
GSE75386 Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons. Mus musculus Stanford University Stanford University 108
GSE75413 Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Mus musculus Fred Hutchinson Cancer Research Centre Fred Hutchinson Cancer Research Centre 93
GSE75659 Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. Mus musculus and Homo sapiens Karolinska Institutet Karolinska Institutet 1318
GSE75748 Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. Homo sapiens Morgridge Institute for Research Morgridge Institute for Research 1776
GSE76381 Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Mus musculus and Homo sapiens Karolinska Institutet Karolinska Institutet 6665
GSE77029 Distinct myeloid progenitor-differentiation pathways identified through single-cell RNA sequencing. Mus musculus Weatheral Institute of Molecular Medicine Weatheral Institute of Molecular Medicine 64
GSE77067 Nuclear RNA-seq of single neurons reveals molecular signatures of activation. Mus musculus The Salk Institute for Biological Studies The Salk Institute for Biological Studies 201
GSE77980 Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. Mus musculus Regeneron Pharmaceuticals Inc. Regeneron Pharmaceuticals Inc. 622
GSE78779 CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Mus musculus Technion - Israel Institute of Technology Technion - Israel Institute of Technology 188
GSE78845 Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control. Mus musculus Karolinska Institutet Karolinska Institutet 312
GSE81682 A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. Mus musculus The University of Cambridge The University of Cambridge 3840
GSE86042 A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Mus musculus Broad Institute Broad Institute 1604
melanoma_pan_cancer Melanoma, Dissociated Tumor Cells: Targeted, Human Pan-Cancer Panel Homo sapiens 10X Genomics 10X Genomics 9265
neurons_2000 2k Brain Cells from an E18 Mouse Mus musculus 10X Genomics 10X Genomics 2440
neurons_900 1k Brain Nuclei from an E18 Mouse Mus musculus 10X Genomics 10X Genomics 1442
neuron_9k 9k Brain Cells from an E18 Mouse Mus musculus 10X Genomics 10X Genomics 11277
nsclc_5gex NSCLC tumor - 5’ gene expression Homo sapiens 10X Genomics 10X Genomics 7802
nuclei_2k 2k Brain Nuclei from an Adult Mouse (>8 weeks) Mus musculus 10X Genomics 10X Genomics 2602
nuclei_900 1k Brain Cells from an E18 Mouse Mus musculus 10X Genomics 10X Genomics 1729
pbmc4k 4k PBMCs from a Healthy Donor Homo sapiens 10X Genomics 10X Genomics 4623
pbmc8k 8k PBMCs from a Healthy Donor Homo sapiens 10X Genomics 10X Genomics 8708
PRJEB8994 Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development. Homo sapiens European Nucleotide Archive EMBL-EBI 372
t_3k 3k Pan T Cells from a Healthy Donor Mus musculus 10X Genomics 10X Genomics 3742
t_4k 4k Pan T Cells from a Healthy Donor Mus musculus 10X Genomics 10X Genomics 4790







More from RIKEN Laboratory for Large-Scale Biomedical Data Technology

SkewC

SkewC a novel quality-assessment method to identify poor quality single-cells in scRNA-seq experiments. The method relies on the measure of skewness of the gene coverage of each single cell as a quality measure.

GitHub